It's safe. All the remote wipe procedure does is remove user profile-specific and/or private data, like purchase/installed apps, notes, call/sms history, browser bookmarks and so on. It does not verify system file "integrity", and what patches and themes do is modify system files.

So go ahead and sign on to your Palm Profile or create a new one if you're using the old profile on another phone.

If you want a truly clean install, if for example you're giving the phone away to a member of your family, just Doctor it. WebOS Doctor ROMs are available on the HP website, or you can use direct links provided in the webOS Internals wiki.